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    SERAC1 serine active site containing 1 [ Homo sapiens (human) ]

    Gene ID: 84947, updated on 14-Nov-2024

    Summary

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    Official Symbol
    SERAC1provided by HGNC
    Official Full Name
    serine active site containing 1provided by HGNC
    Primary source
    HGNC:HGNC:21061
    See related
    Ensembl:ENSG00000122335 MIM:614725; AllianceGenome:HGNC:21061
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    The protein encoded by this gene is a phosphatidylglycerol remodeling protein found at the interface of mitochondria and endoplasmic reticula, where it mediates phospholipid exchange. The encoded protein plays a major role in mitochondrial function and intracellular cholesterol trafficking. Defects in this gene are a cause of 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome (MEGDEL). Two transcript variants, one protein-coding and the other non-protein coding, have been found for this gene. [provided by RefSeq, Aug 2012]
    Expression
    Ubiquitous expression in testis (RPKM 4.2), adrenal (RPKM 3.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SERAC1 in Genome Data Viewer
    Location:
    6q25.3
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (158109519..158168262, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (159355719..159413646, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (158530551..158589294, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene sorting nexin 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17730 Neighboring gene RNA, U6 small nuclear 786, pseudogene Neighboring gene CRISPRi-validated cis-regulatory element chr6.5510 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158394739-158395292 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158402145-158402660 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158402661-158403176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158420467-158420966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25345 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158447101-158447788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158447789-158448476 Neighboring gene SYNJ2 intronic transcript 1 Neighboring gene Sharpr-MPRA regulatory region 12557 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158458586-158459280 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158461967-158462502 Neighboring gene synaptojanin 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158470498-158471112 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:158490014-158491213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158492197-158492760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158492761-158493322 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158516915-158517415 Neighboring gene MPRA-validated peak6269 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17733 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158604741-158605243 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158604236-158604740 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:158615403-158616003 Neighboring gene general transcription factor IIH subunit 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17735 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:158653118-158653990 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25348 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25349 Neighboring gene signal recognition particle 72 pseudogene 2 Neighboring gene TUB like protein 4

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. First description of the MEGDEHL syndrome in the Tunisian population via whole-exome sequencing: Novel nonsense mutation in SERAC1 gene.
      Title: First description of the MEGDEHL syndrome in the Tunisian population via whole-exome sequencing: Novel nonsense mutation in SERAC1 gene.
    2. Severe neonatal MEGDHEL syndrome with a homozygous truncating mutation in SERAC1.
      Title: Severe neonatal MEGDHEL syndrome with a homozygous truncating mutation in SERAC1.
    3. Our study indicates that the cochlear CHI is a phenotypic feature of the RRM2B and SERAC1 related defects.
      Title: Congenital cochlear deafness in mitochondrial diseases related to RRM2B and SERAC1 gene defects. A study of the mitochondrial patients of the CMHI hospital in Warsaw, Poland.
    4. Two novel SERAC1 mutations were identified in two cases of dystonia, 3-methylglutaconic aciduria and intellectual disability syndrome.
      Title: Novel mutations in SERAC1 gene in two Indian patients presenting with dystonia and intellectual disability.
    5. mutations in the phosphatidylglycerol remodelling enzyme SERAC1 can cause juvenile-onset complicated hereditary spastic paraplegia (cHSP) clusters
      Title: SERAC1 deficiency causes complicated HSP: evidence from a novel splice mutation in a large family.
    6. Several different SERAC1 variants were identified from individuals with Deafness-Dystonia syndrome.
      Title: Progressive deafness-dystonia due to SERAC1 mutations: A study of 67 cases.
    7. Here we report two new Turkish sibling patients affected with MEGDEL syndrome due to SERAC1 gene mutation.
      Title: Two Turkish siblings with MEGDEL syndrome due to novel SERAC1 gene mutation.
    8. Infantile mitochondrial hepatopathy is a cardinal feature of MEGDEL syndrome (3-methylglutaconic aciduria type IV with sensorineural deafness, encephalopathy and Leigh-like syndrome) caused by novel mutations in SERAC1.
      Title: Infantile mitochondrial hepatopathy is a cardinal feature of MEGDEL syndrome (3-methylglutaconic aciduria type IV with sensorineural deafness, encephalopathy and Leigh-like syndrome) caused by novel mutations in SERAC1.
    9. During the course of this project a parallel study identified mutations in SERAC1 as the genetic cause of the disease in 15 patients with MEGDEL syndrome, which was compatible with the clinical and biochemical phenotypes of the patient described here.
      Title: Exome sequencing identifies a new mutation in SERAC1 in a patient with 3-methylglutaconic aciduria.
    10. Data identify SERAC1 as a key player in the phosphatidylglycerol remodeling that is essential for both mitochondrial function and intracellular cholesterol trafficking.
      Title: Mutations in the phospholipid remodeling gene SERAC1 impair mitochondrial function and intracellular cholesterol trafficking and cause dystonia and deafness.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ14917, FLJ30544

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in extracellular matrix organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in intracellular cholesterol transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in phosphatidylglycerol acyl-chain remodeling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in phospholipid biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular matrix IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondria-associated endoplasmic reticulum membrane contact site IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrial outer membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion HTP PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein SERAC1
    Names
    serine active site-containing protein 1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_032889.1 RefSeqGene

      Range
      5019..63762
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_032861.4 → NP_116250.3  protein SERAC1

      See identical proteins and their annotated locations for NP_116250.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and is the protein-coding variant.
      Source sequence(s)
      AK027823, BC001705
      Consensus CDS
      CCDS5255.1
      UniProtKB/Swiss-Prot
      Q49AT1, Q5VTX3, Q6PKF3, Q96JX3
      UniProtKB/TrEMBL
      A0A2R8Y3S0
      Related
      ENSP00000496731.1, ENST00000647468.2
      Conserved Domains (2) summary
      COG0596
      Location:386 → 592
      MhpC; Pimeloyl-ACP methyl ester carboxylesterase [Coenzyme transport and metabolism, General function prediction only]
      cl21494
      Location:396 → 540
      Abhydrolase; alpha/beta hydrolases

    RNA

    1. NR_073096.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks two alternate internal exons and has an alternate 3' exon structure compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL590703, BC048335, DA232092
      Related
      ENST00000606965.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      158109519..158168262 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006715586.4 → XP_006715649.1  protein SERAC1 isoform X3

      See identical proteins and their annotated locations for XP_006715649.1

      UniProtKB/TrEMBL
      A0A2R8YCL0
      Related
      ENSP00000493723.1, ENST00000646208.1
      Conserved Domains (2) summary
      COG0596
      Location:316 → 522
      MhpC; Pimeloyl-ACP methyl ester carboxylesterase [Coenzyme transport and metabolism, General function prediction only]
      cl21494
      Location:326 → 470
      Abhydrolase; alpha/beta hydrolases

    2. XM_047419421.1 → XP_047275377.1  protein SERAC1 isoform X2

    3. XM_024446573.2 → XP_024302341.1  protein SERAC1 isoform X1

      UniProtKB/Swiss-Prot
      Q49AT1, Q5VTX3, Q6PKF3, Q96JX3
      UniProtKB/TrEMBL
      A0A2R8Y3S0

    4. XM_011536198.4 → XP_011534500.1  protein SERAC1 isoform X3

      See identical proteins and their annotated locations for XP_011534500.1

      UniProtKB/TrEMBL
      A0A2R8YCL0
      Conserved Domains (2) summary
      COG0596
      Location:316 → 522
      MhpC; Pimeloyl-ACP methyl ester carboxylesterase [Coenzyme transport and metabolism, General function prediction only]
      cl21494
      Location:326 → 470
      Abhydrolase; alpha/beta hydrolases

    RNA

    1. XR_007059349.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      159355719..159413646 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356600.1 → XP_054212575.1  protein SERAC1 isoform X3

    2. XM_054356599.1 → XP_054212574.1  protein SERAC1 isoform X2

    3. XM_054356598.1 → XP_054212573.1  protein SERAC1 isoform X1

      UniProtKB/Swiss-Prot
      Q49AT1, Q5VTX3, Q6PKF3, Q96JX3

    4. XM_054356601.1 → XP_054212576.1  protein SERAC1 isoform X3

    RNA

    1. XR_008487454.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96JX3.1 GenPept UniProtKB/Swiss-Prot:Q96JX3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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